[gmx-users] REMD error

[Mark Abraham]

On 12/01/2012 5:29 PM, bharat gupta wrote:
> Thanks for the advice I re-complied everything again with static 
> libraries and the installation went fine. But while executing the 
> following command I am again getting error :-
>
>
> mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v
>
>
> Fatal error:
> The number of nodes (1) is not a multiple of the number of simulations (3)
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>
> Halting program mdrun_mpi
>
> gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>
>
> I am trying to simulate 5 replicas and I have 4 cpu .

See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps 
point 2. You cannot simulate an arbitrary number of replicas on an 
arbitrary number of processors.

Mark

>
>
>
> On Thu, Jan 12, 2012 at 1:37 PM, lina <lina.lastname at gmail.com 
> <mailto:lina.lastname at gmail.com>> wrote:
>
>     On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:
>
>         Hi,
>
>         I am trying to run a REMD of a peptide. But while executing the
>         following command after nvt and npt equilibration , I am
>         getting the
>         following error:-
>
>         mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
>         mdrun_mpi: error while loading shared libraries:
>         libgmx_mpi.so.6: cannot
>         enable executable stack as shared object requires: Permission
>         denied
>
>
>     Can you run a normal md smoothly?
>     try:
>     mdrun_mpi mdrun -deffnm prefix_0
>
>     if it works, then some of your trajectories not sound. means
>     system does not equilibrium well.
>
>
>
>         Can anybody suggest me how could I rectify this error.
>
>         --
>         Bharat
>
>
>     -- 
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>
>
> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
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>
>
>

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